LAMMPS (20 Jun 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide, run for 8ps in NVT

units           real
atom_style      full

pair_style      lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style    pppm 0.0001

read_data       data.peptide
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors

neighbor        2.0 bin
neigh_modify    delay 5

thermo          50
#dump            dump1 all atom 100 peptide.dump

timestep        8

run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
Respa levels:
  1 = bond angle
  2 = dihedral improper pair
  3 = kspace

fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
fix             cor all filter/corotate m 1.0
  19 = # of size 2 clusters
  0 = # of size 3 clusters
  3 = # of size 4 clusters
  0 = # of size 5 clusters
  646 = # of frozen angles
run             1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 4312 960
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.87 | 17.05 | 17.26 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0     190.0857   -6442.7438    70.391457   -5237.4338    20361.984 
      50    239.47667   -7205.1005    1092.7664   -4682.5237   -23733.122 
     100    244.63889   -6788.1152    422.96733   -4904.5161    16457.756 
     150    239.36917   -7258.7053    967.87775   -4861.6589   -13526.261 
     200    255.14702   -6864.0525    604.58036   -4736.1009      11013.1 
     250    252.72919   -7303.0966    898.11178   -4896.0494   -8480.8766 
     300    250.66477   -6989.2603    652.83649   -4839.8141    6209.3375 
     350    243.30794   -7218.8575    838.31977   -4927.8525   -5180.4928 
     400     256.3573    -7090.677    706.24197   -4853.8377     3302.577 
     450    246.15776    -7274.574    834.31676    -4970.557    -3427.971 
     500    256.28473   -7082.1447    735.42828   -4816.5524     2846.086 
     550    251.32327    -7341.739    812.64934   -5028.5484   -1786.9277 
     600    254.57737   -7152.3448    740.52534   -4891.8494    825.91675 
     650    244.95305   -7207.1136    790.67659   -4953.9295   -520.79769 
     700     249.4984   -7204.2699    779.06969   -4935.5544   -940.75384 
     750    248.46962   -7232.1037     791.6642   -4956.9361   -548.12171 
     800     260.2974   -7293.1982    793.23282   -4945.8435     -1171.26 
     850    249.79023   -7258.3759    823.56789   -4943.4198   -499.76275 
     900    249.97237   -7267.0584    784.57992   -4990.0028   -271.33531 
     950    251.29018   -7261.0642      823.467   -4937.2534    -538.7168 
    1000    246.05777   -7285.0948    847.90892   -4968.0826   -2613.1854 
Loop time of 94.6835 on 4 procs for 1000 steps with 2004 atoms

Performance: 7.300 ns/day, 3.288 hours/ns, 10.562 timesteps/s
37.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 33.389     | 78.508     | 94.639     | 294.1 | 82.92
Bond    | 0.39957    | 1.104      | 1.4443     |  40.6 |  1.17
Kspace  | 0.53324    | 1.2631     | 1.5137     |  37.5 |  1.33
Neigh   | 1.2668     | 3.011      | 3.5942     |  58.0 |  3.18
Comm    | 3.4563     | 8.8707     | 11.494     | 107.9 |  9.37
Output  | 0.000435   | 0.0017425  | 0.004136   |   3.4 |  0.00
Modify  | 0.59335    | 1.4123     | 1.6921     |  39.8 |  1.49
Other   |            | 0.5129     |            |       |  0.54

Nlocal:    501 ave 515 max 476 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost:    6681.5 ave 6740 max 6634 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs:    176872 ave 182642 max 168464 min
Histogram: 1 0 0 0 0 0 1 1 0 1

Total # of neighbors = 707486
Ave neighs/atom = 353.037
Ave special neighs/atom = 2.34032
Neighbor list builds = 200
Dangerous builds = 200
unfix           cor
unfix           1




Please see the log.cite file for references relevant to this simulation

Total wall time: 0:01:53
